AIC model selection results, with the different models sorted from best to worse fit.

<p>The term of interest in testing for divergent selection is the Species^*Host interaction. For survival, the interaction between Species and Host was significant in the best fit AIC model (F_1,87 = 4.27, p = 0.042), and significant or marginally insignificant in other models (full factorial model, F_1,29 = 3.03, p = 0.09; second and third best models picked by AIC that included the interaction, F_1,58 = 3.72, p = 0.06, F_1,58 = 4.04, p = 0.049, respectively). For fecundity, the interaction was significant in the best AIC model (F_1,120 = 11.14, p = 0.001), and in other models (p<0.01 for interaction terms in second and third best AIC models, and in a full factorial model).</p

Morphological divergence between walking-stick taxon pairs.

<p>We consider here ten traits that were examined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone.0001907-Nosil5" target="_blank">[71]</a>, as well as principle components (PC) axes generated from all these ten traits or from the colour variables only. Divergence in trait means between hosts was often statistically significant for all three taxon pairs (testing using F-ratios in ANOVA analyses), but the magnitude of divergence tended to be greater for the species pair than the ecotype pairs (particularly for colour traits, which are known to be under host-specific selection). Mean trait values are shown for <i>Ceanothus</i> (C) and <i>Adenostoma</i> (A), along with the difference between means (D = mean on <i>Ceanothus</i> minus mean on <i>Adenostoma</i>). Also shown is the percent difference between means (% <b>Δ</b>), calculated as 1–(smaller value/larger value). Thus, larger values of % <b>Δ</b> represent larger differences between taxon pairs (due to negative means, this calculation was not conducted for PC axes). This calculation is in bold to emphasize standardized differences between taxon pairs. Traits are as follows: 1 = body hue, 2 = body saturation, 3 = body brightness, 4 = stripe hue, 5 = stripe saturation, 6 = stripe brightness, 7 = head width, 8 = femur length, 9 = thorax width, 10 = body length, 11 = PC1 using all ten traits, 12 = PC2 using all ten traits, 13 = PC1 using only colour variables, 14 = PC2 using only colour variables.</p

The number of niche dimensions subject to divergent selection and speciation of <i>Timema</i> walking-stick insects.

<p>Depicted are the two ecotype pairs and the species pair studied for the degree of phenotypic and evolutionary divergence in relation to the number of niche dimensions subject to divergent selection. A1 and C1 refer to ecotypes of <i>T. cristinae</i> (A = <i>Adenostoma</i> and C = <i>Ceanothus</i> hereafter). A2 and C2 refer to ecotypes of <i>T. podura</i>. A3 and C3 refer to the species pair <i>T. podura</i> and <i>T. chumash</i>, respectively. The ecotype pairs exhibit weaker divergence in morphology, host preference, and mtDNA than the species pair, and are also subject to divergent selection on fewer niche dimensions. A) Photographs of the three taxon pairs, and divergence in colour-pattern between them (brightness contrast, mean±95% C.I.). Host plants are also shown. B) Summary of divergence in host plant preferences and mtDNA (colours represent host plant use). Δ%C refers to the difference between each taxon pair in the percent of individuals choosing <i>Ceanothus</i> over <i>Adenostoma</i> in host preference trials [data from 78, 72, and the current study for <i>T. cristinae</i> ecotypes, <i>T. podura</i> ecotypes, and the species pair, respectively]. The phylogenetic trees are schematic for simplicity. The patterns depicted were robust to alternative methods for tree construction <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone.0001907-Nosil6" target="_blank">[75]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone.0001907-Law1" target="_blank">[81 for details]</a>. C) The nature of selection on crypsis and physiology for each taxon pair. For crypsis, the term ‘survival’ is used as a general y-axis label, representing the fitness of each insect host form on each host species. For ecotypes, the y-axes specifically represent 1- the proportion of insects eaten in predation trials with scrub jays <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone.0001907-Sandoval3" target="_blank">[data from 72]</a>. For the species pair, the y-axis specifically represents the proportion of each insect species on each host plant at the end of the field experiment (shown in more detail in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone-0001907-g002" target="_blank">Fig. 2</a>). Further evidence that selection is exerted by visual predation stems from the observation that: (a) survival was measured using predation trials, or (b) divergent selection in manipulative field experiments was detected in the presence, but not in the absence, of visual predation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone.0001907-Nosil4" target="_blank">[see also 70]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone.0001907-Nosil5" target="_blank">[71]</a>. For physiology, the y-axis represents lifetime fecundity in all cases (data on survival for the species pair are also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone-0001907-g002" target="_blank">Fig. 2</a>). The data depicted can be used to infer the presence versus absence of divergent selection, but should not be used to quantitatively compare the strength of selection (because somewhat different experimental procedures were used among taxa). For simplicity, error bars were removed for the current figure, but are depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone-0001907-g002" target="_blank">Fig. 2</a>. See text for statistical details.</p

Host preferences and tests for divergent selection on crypsis and physiology.

<p>A) Host-plant preferences of <i>Timema</i> collected from <i>Adenostoma</i> (<i>T. podura</i>) or <i>Ceanothus</i> (<i>T. chumash</i>). Shown for each insect species is the percent of individuals choosing each host species in host choice trials. Numbers of individuals are denoted above the bars. Each <i>Timema</i> species preferred its native host. B) Results of the predation experiment. <i>T. podura</i> and <i>T. chumash</i> were released at equal proportion onto <i>Ceanothus</i> and <i>Adenostoma</i> bushes. Four weeks later the relative proportion of each insect species had diverged, but to a much larger extent when predation was present versus absent. Shown is the proportion of <i>T. chumash</i> (±1 S.E.) on each host species. C) Results of the physiology experiment. Norm-of-reaction plots showing means and standard errors (±1 S.E.) of survival of walking-sticks from <i>Ceanothus</i> or <i>Adenostoma</i> raised on their native or the alternative host-plant species. Survival was estimated as the mean number of insects observed alive within an enclosure, averaged across the multiple census periods. Physiological trade-offs in host plant use were evident.</p

Significance testing of the terms in the best AIC model (Table 2 for details), for survival and fecundity (the term of interest in testing for divergent selection is the Species*Host interaction, which was significant for both survival and fecundity, and is indicated in bold).

<p>Significance testing of the terms in the best AIC model (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001907#pone-0001907-t002" target="_blank">Table 2</a> for details), for survival and fecundity (the term of interest in testing for divergent selection is the Species*Host interaction, which was significant for both survival and fecundity, and is indicated in bold).</p

Flaxman_Data

.zip archive of raw data used in publication figure

HPcorrsummary

HPcorrsummar

Datafile

This file is a .zip compressed archive containing subdirectories each having raw data and analysis scripts for producing the 7 figures in the paper

Simulated phenotypes based on the Rhagoletis GBS data

This compressed folder contains the simulated data sets where Rhagoletis pomonella GBS data were used as the starting point. It contains two gemma formatted genotype files (geno_sims.txt and geno592r_sims.txt) that contain the underlying genotypic data for the base simulations and those with replicated genotypes, respectively. The remaining files are named based on the simulations condition (simsN): 1, h2=0.3, L = 100; 2, h2=0.3, L=10; 3, h2=0.05, L=100; 4, h2=0.05, L=10; 5, h2=0.3, L=1000; and 6, h2=0.05, L=1000. The general file types are as follows: pheno* = gemma formatted phenotype file with one column per simulated phenotypic data set, bv* = breeding values (expected phenotypic values) for each individual based on the genotypic data, effect* = phenotypic effect sizes for causal variants, functvar* = a list of the causal variants (by SNP number, and in the same order as in effect*)

Summary scripts

This compressed directory contains the perl scripts used to summarize (1) the posterior distribution of genome-level genetic architecture parameters (calcpost*), and (2) SNP specific selection coefficients (summarizeSNP*pl)